1.7. EMBOSS Installation: Platform-specific Concerns

1.7.1. Linux RPM Distributions

These distributions include Fedora, [Open]SuSE, Mandriva, CentOS and RedHat.

1.7.1.1. General Prerequisites

Make sure you have the X11 development files installed before you configure EMBOSS.

The latest Linux distributions use the XORG version of X11. For these type one of:

rpm -q xorg-x11-proto-devel

rpm -q xorg-x11-devel

to check whether the package is installed. If not then install the relevant RPM from your distribution DVD/CDs using one of:

rpm -i filename.rpm

yum packagename (if available)

If you wished to see, for example, all the xorg-x11 packages installed on your system you would type:

rpm -qa "xorg-x11*"

Older Linux distributions use the XFree86 version of X11.

For these, type:

rpm -q XFree86-devel

to see whether the development files are installed.

1.7.1.2. PNG prerequisites

PNG support is optional; however, it is required if you intend using the Jemboss graphical interface. You need to make sure that the following libraries and development files have been installed from your distribution DVD/CDs:

zlib

zlib-devel

libpng

libpng-devel

gd

gd-devel

You can check to see they're there using the rpm -q or rpm -qa command(s) as above. Use the rpm -ifilename.rpm command to install them if necessary (or yum packagename or a graphical package manager if available).

1.7.1.3. PDF prerequisites

PDF support is optional. You need to make sure that the following library and its development files have been installed from your distribution DVD/CDs:

libharu

libharu-devel

You can check to see they're there using the rpm -q or rpm -qa command(s) as above. Use the rpm -ifilename.rpm command to install them if necessary (or yum packagename or a graphical package manager if available).

1.7.1.4. Java

Java is optional; however, it is required if you intend using the Jemboss graphical interface. Many Linux distributions contain either outdated versions of Java or support only via the GNU gcj compiler. Using the former is not recommended: using the latter will not work at all! Some current Linux distributions are supplied with the OpenJDK package. This should work with Jemboss and we will aim to sort out any incompatibilities should they arise. The latest version of Java from java.sun.com will almost certainly work. At the time of writing this is version J2SE 6.0. It is essential that you install the JDK package and not just the JRE. We further recommend that you use the Linux self-extracting file version and not the Linux RPM in self-extracting file version. A typical installation would go like this:

cd /usr/local

sh jdk-6u14-linux-i586.bin

rm -f java; ln -s jdk1.6.0_14 java

This would install Java under /usr/local and replace any existing symbolic link called java with a new one.

You should then add /usr/local/java/bin to the start of your PATH to avoid other Java installations being picked up in preference and, if using a (t)csh shell, rehash. Jemboss installation examples in this book assume that the Java binaries are in /usr/local/java/bin unless otherwise specified.

1.7.2. Linux Debian Distributions

These distributions include Debian itself and derivatives such as Ubuntu.

1.7.2.1. General Prerequisites

Make sure you have the X11 development files installed before you configure EMBOSS. You can use the following command to check:

dpkg --list x-dev

Install the x-dev package, if necessary, using the dpkg -i command or a graphical package manager.

1.7.2.2. PNG prerequisites

PNG support is optional; however, it is required if you intend using the Jemboss graphical interface. You need to make sure that the following libraries and development files have been installed from your distribution DVD/CDs:

zlib1g

zlib1g-dev

libpng12-0

libpng12-dev

libgd2-xpm

libgd2-xpm-dev

You can check to see they're there using the dpkg --list command as above. Use the dpkg -ifilename.deb command to install them if necessary. Alternatively use a graphical package manager for installation.

1.7.2.4. Java

Everything that was said for Linux RPM Distributions also holds for Debian distributions.

1.7.3. MacOSX

These instructions refer to the 10.6 & 10.5 versions of MacOSX although similar principles apply to 10.4 & 10.3.

Caution

Also note that the EMBOSS developers can only realistically support the package on a virgin MacOSX installation.

However, there are two MacOSX projects that provide pre-bundled EMBOSS distributions. They are the MacPorts project http://www.macports.org and the FINK project http://www.finkproject.org. If you choose to install EMBOSS from either of these sources then you will obviously not be following the standard UNIX methods for installation described earlier: in which case you should use the FINK or MacPorts documentation and support contacts (should anything go wrong). You may not require the information presented below, with the exception of the need for the Xcode tools. On the other hand, if you use (e.g.) the MacPorts GD / PNG libraries and are otherwise compiling the standard EMBOSS source code yourself, then by all means contact the EMBOSS developers for support if you have installation problems.

1.7.3.1. General Prerequisites

It is essential to have installed the Xcode tools, X11 (if provided) and any SDK packages from your distribution DVD. Not all of these may be installed by default so insert your DVD if necessary and do a custom installation and ensure their check boxes are ticked. To be sure of getting the latest version of (e.g.) Xcode then you will need to register as a developer at http://connect.apple.com.

1.7.3.2. PNG prerequisites

PNG support is optional. It is, however, essential if you intend installing the Jemboss graphical interface. You have the choice of downloading gd and libpng and their dependencies from the MacPorts or FINK projects, or compiling from source code. For the former see the instructions on the respective website, for the latter see below.

We recognize, from support queries, that there are a greater proportion of MacOSX users who are unfamiliar with the UNIX command line compared to users of other UNIX flavours. Experienced hackers will have to forgive us for giving verbose installation instructions for this platform.

Installation of the PNG libraries and development files is done first, then the installation of the gd libraries and development files. Both are required for PNG support. So, first for PNG itself.

We recommend you download the gz file i.e. gd-2.0.35.tar.gz It is useful to make a gd directory (mkdir gd) and put the file in there.

Uncompress the gd-2.0.35.tar.gz file:

gunzip gd-2.0.35.tar.gz

Untar the resulting tar file.

tar xf gd-2.0.35.tar

This will create a gd-2.0.35 directory. Move into that directory.

cd gd-2.0.35

Configure the software using the standard GNU configure file in the gd-2.0.35 directory

./configure --without-freetype --without-fontconfig

MacOSX does not ship with freetype or fontconfig support and EMBOSS does not require them. If you want such support included then install their libraries separately and adjust the configuration by removal of the --without statements.

1.7.3.4. Java

Java is optional; however, it is required if you intend using the Jemboss graphical interface. Both Java and the Java SDK are required and are provided on your MacOSX DVD. Note that they may not be installed using a standard system installation. Your MacOSX installation DVD may contain them so reinsert the DVD and do a custom installation as necessary.

1.7.4. IRIX

1.7.4.1. General Prerequisites

We recommend that you use the IRIX cc compiler as this will provide the greatest level of code optimization. The GNU gcc compiler is a suitable alternative. The EMBOSS configuration, like most configure scripts, will choose the gcc compiler by default if both compilers are available. To force use of cc you can type:

setenv CC cc [tcsh/csh]

CC=cc [sh/bash]

export CC

before configuring EMBOSS. There is a special configuration switch provided for the IRIX compiler in the EMBOSS configuration. Namely:

--with-sgiabi=

This can have the values:

n32m3

n32m4

64m3

64m4

n32 refers to 32-bit processors and 64 to 64-bit processors. m3 refers to the Mips3 compiler and m4 to the Mips4 compiler. So, if you are using a 32-bit processor with the Mips3 compiler then add the following switch to your configuration command:

./configure--with-sgiabi=n32m3[ other optional switches ]

1.7.4.2. PNG prerequisites

PNG is optional. It is, however, required if you intend using the Jemboss graphical interface.

1.7.4.4. Java

Java is optional; however, it is required if you intend using the Jemboss graphical interface.

Java for IRIX used to be available from the SGI Cool Software Index, however this has now been removed; you may have to search the internet to find a copy.

Caution

You must install the JDK and not just the JRE. Their latest version was 1.4.1_06 at the time of writing. This is acceptable for EMBOSS, but rather outdated. It will usually install into /usr/java2.

1.7.5. Tru64

1.7.5.1. General Prerequisites

We recommend that you use the OSF1 cc compiler as this will provide the greatest level of code optimization. The GNU gcc compiler is a suitable alternative. The EMBOSS configuration, like most configure scripts, will choose the gcc compiler by default if both compilers are available. To force use of cc you can type:

1.7.5.4. Java

Java is optional; however, it is required if you intend using the Jemboss graphical interface. Java for Tru64 can be downloaded from http://www.hp.com.

Caution

You must install the JDK and not just the JRE. The latest version was 1.4.2-08 at the time of writing. This is acceptable for EMBOSS, but rather outdated.

1.7.6. Solaris

These instructions refer to Solaris 10, although they should apply equally well to other versions of this operating system.

1.7.6.1. General Prerequisites

We recommend that you use the Solaris cc compiler as this will provide the greatest level of code optimization. The GNU gcc compiler is a suitable alternative. The EMBOSS configuration, like most configure scripts, will choose the gcc compiler by default if both compilers are available. To force use of cc you can type:

setenv CC cc [tcsh/csh]

CC=cc; export CC [sh/bash]

before configuring EMBOSS.

If you are using gcc then the version available on the companion CD is suitable. If using the gcc version from http://www.sunfreeware.com then you may need to re-run the header modification script fixincludes in that distribution.

/usr/ccs/bin must be in your path; otherwise the ar and make programs will not be found.

You should have the GNU tar program installed. The Solaris-supplied tar is too limited and may not extract the Jemboss files correctly. This can be downloaded from ftp://ftp.gnu.org/gnu/tar/:

./configure --prefix=/usr/local/

make install

Add /usr/local/bin to the start of your PATH and, if using a [t]csh shell, rehash.

1.7.6.2. PNG prerequisites

You should install PNG using the files supplied by http://www.sunfreeware.com. The main packages are gd and libpng, however there are many dependencies so you will probably find yourself having to install all these packages:

expat-2.0.1-sol10-sparc-local.gz

fontconfig-2.4.2-sol10-sparc-local.gz

freetype-2.3.9-sol10-sparc-local.gz

jpeg-6b-sol10-sparc-local.gz

libiconv-1.11-sol10-sparc-local.gz

xpm-3.4k-sol10-sparc-local.gz

libpng-1.2.38-sol10-sparc-local.gz

gd-2.0.35-sol10-sparc-local.gz

Use (e.g.)

gunzip expat-2.0.1-sol10-sparc-local.gz

pkgadd -d expat-2.0.1-sol10-sparc-local

The packages will be installed under the /usr/local directory tree.

Alternatively, to avoid all the dependencies, which EMBOSS does not require, you should consider compiling PNG support yourself using the "Installing from source code" instructions (Section 1.9, “PNG support: Installing from Source Code”). If you do this then, to avoid conflict with sunfreeware files, install them in a directory tree other than /usr/local (e.g. use ./configure -prefix=/usr/local/png for the PNG packages and then configure EMBOSS using ./configure -with-pngdriver=/usr/local/png [+ any other options]).